Variant report

Variant	rs10467972
Chromosome Location	chr15:40848724-40848725
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40838014..40841452-chr15:40845857..40849279,3	MCF-7	breast:
2	chr15:40848640..40851135-chr15:40883399..40886206,2	K562	blood:

Extended variants
information (count: 92 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10400825	0.90[EUR][1000 genomes]
rs11070284	0.85[EUR][1000 genomes]
rs11070285	0.80[JPT][hapmap]
rs11070286	0.80[JPT][hapmap]
rs11070292	0.83[CEU][hapmap]
rs11629680	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11632061	0.87[CHB][hapmap]
rs11632370	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs11637239	0.91[EUR][1000 genomes]
rs11638742	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs11852694	0.80[JPT][hapmap]
rs11854763	0.85[EUR][1000 genomes]
rs11854986	0.80[JPT][hapmap]
rs11855334	0.80[JPT][hapmap]
rs11856438	0.80[JPT][hapmap]
rs11858113	0.80[JPT][hapmap]
rs12438955	0.85[EUR][1000 genomes]
rs12440468	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12592882	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12594548	0.83[CHB][hapmap]
rs12595610	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs12708401	0.85[EUR][1000 genomes]
rs12911738	0.91[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs12912058	0.91[CEU][hapmap];0.89[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs12912339	0.85[EUR][1000 genomes]
rs12914743	0.80[JPT][hapmap]
rs12915109	0.82[EUR][1000 genomes]
rs12916082	0.82[EUR][1000 genomes]
rs16970851	0.80[JPT][hapmap]
rs17747351	0.91[CEU][hapmap]
rs1901775	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2278888	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304580	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs2412531	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs2412532	0.88[CHB][hapmap];0.80[JPT][hapmap]
rs2412534	0.88[CHB][hapmap]
rs2412541	0.91[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs2412544	0.80[JPT][hapmap]
rs2619681	0.91[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs2924388	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs2959536	0.83[CHB][hapmap]
rs3092978	0.91[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs35047458	0.80[JPT][hapmap]
rs3751653	0.80[JPT][hapmap]
rs4417527	0.91[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs4420508	0.85[EUR][1000 genomes]
rs4439732	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4923876	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs4924478	0.80[JPT][hapmap]
rs4924481	0.83[CHB][hapmap];0.80[JPT][hapmap];0.85[YRI][hapmap]
rs4924484	0.84[EUR][1000 genomes]
rs4924487	0.83[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs4924488	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4924491	0.81[EUR][1000 genomes]
rs4924500	0.89[CEU][hapmap];0.94[JPT][hapmap]
rs55640412	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492957	0.85[EUR][1000 genomes]
rs6492958	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs6582	0.83[CHB][hapmap]
rs66885559	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7161938	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs7161968	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7162319	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7162509	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7164289	0.91[EUR][1000 genomes]
rs7167417	0.91[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs7168873	0.81[EUR][1000 genomes]
rs7171260	0.91[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs7171945	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7172947	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7176974	0.85[EUR][1000 genomes]
rs7177192	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7178486	0.85[EUR][1000 genomes]
rs72733486	0.86[EUR][1000 genomes]
rs7494968	0.83[CHB][hapmap]
rs8026605	0.80[JPT][hapmap]
rs8028999	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029384	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs8031057	0.83[EUR][1000 genomes]
rs8035775	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs8037417	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8037804	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs8040502	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs8042729	0.88[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs896795	0.88[CHB][hapmap];0.85[YRI][hapmap]
rs896796	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs936580	0.80[EUR][1000 genomes]
rs9806221	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10467972	ZFYVE19	cis	cerebellum	SCAN
rs10467972	C15orf57	cis	lymphoblastoid	seeQTL
rs10467972	RMDN3	cis	Muscle Skeletal	GTEx
rs10467972	FAM82A2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40821800-40856400	Weak transcription	Colon Smooth Muscle	Colon
2	chr15:40822600-40856400	Weak transcription	Small Intestine	intestine
3	chr15:40828000-40856600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:40831600-40856600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:40838000-40856400	Weak transcription	A549	lung
6	chr15:40838600-40852800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:40838600-40855600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr15:40839200-40849000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:40839200-40849000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:40839200-40849600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:40839200-40850000	Strong transcription	Fetal Thymus	thymus
12	chr15:40839400-40849600	Strong transcription	HMEC	breast
13	chr15:40839400-40850000	Strong transcription	Fetal Intestine Large	intestine
14	chr15:40839600-40849800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr15:40840000-40856400	Weak transcription	Fetal Brain Female	brain
16	chr15:40840000-40856600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:40840400-40850600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:40840600-40848800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr15:40842000-40849800	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr15:40842000-40849800	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr15:40842000-40849800	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:40842400-40849000	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:40842400-40856200	Weak transcription	Colonic Mucosa	Colon
24	chr15:40842600-40849400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:40843200-40848800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr15:40843200-40856400	Weak transcription	Fetal Heart	heart
27	chr15:40843600-40849600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:40843600-40850000	Strong transcription	Osteobl	bone
29	chr15:40843800-40849000	Strong transcription	Liver	Liver
30	chr15:40843800-40850000	Strong transcription	Placenta	Placenta
31	chr15:40843800-40856400	Weak transcription	HSMMtube	muscle
32	chr15:40844800-40849400	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr15:40845000-40849600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:40845000-40849600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr15:40845000-40849600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr15:40845000-40849800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:40845200-40849400	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:40845200-40849600	Strong transcription	Primary T cells from cord blood	blood
39	chr15:40845200-40849600	Strong transcription	NHEK	skin
40	chr15:40845400-40848800	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr15:40845400-40848800	Strong transcription	Dnd41	blood
42	chr15:40845400-40849400	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr15:40845600-40850600	Genic enhancers	K562	blood
44	chr15:40845800-40849600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:40846000-40855600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:40846200-40850800	Weak transcription	Pancreas	Pancrea
47	chr15:40846200-40851000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr15:40846200-40855000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:40846200-40856200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr15:40846400-40849200	Weak transcription	Fetal Kidney	kidney

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